Abstract Congenital heart disease is a leading cause of death in children, exacting a substantial emotional and economic toll. To study the mechanisms of congenital heart disease, most research has sought to identify genetic mutations in human patients or to dissect cardiac developmental pathways in animal models, but the knowledge garnered has not suggested clear strategies for treatment or prevention. On the other hand, individuals who have the same mutation commonly have presentations ranging from normal to life-threatening. Such experiments of nature suggest that unknown factors modify the phenotypic expression of a mutation. If these factors were understood, they might be therapeutically mimicked to prevent or ameliorate disease in others. Our long term goal hence is to dissect the basis of incomplete penetrance and phenotypic pleiotropy. Mutation of the cardiac transcription factor NKX2-5 was one of the first among more than a dozen genes known to cause human congenital heart disease. NKX2-5 mutant phenotypes include normal hearts, simple atrial and ventricular septal defects (ASD, VSD), and complex malformations like double outlet right ventricle. To characterize the sources of phenotypic variability, we crossed inbred mouse strains to show how genetic and non-genetic factors affect the development of heart defects. Preliminary linkage analyses in the F2 intercrosses have identified multiple modifier loci for individual defects and led to a candidate VSD modifier gene. In addition, one cross replicates the commonly reported human epidemiologic association of older maternal age with an increased risk of congenital heart defects independent of any chromosomal abnormality. The maternal age effect strongly interacts with a modifier locus on chromosome 10. Thus, our guiding hypothesis is that modifier genes buffer cardiac developmental pathways against genetic and environmental insults in the majority of a population while directing the manifestation of disease in a few. Characterization of the genetic architecture of congenital heart disease in a mouse model will lead to a deeper understanding of its multifactorial basis and possibly novel strategies for prognosis and prevention.